Discovery of novel small RNAs in the quest to unravel genome complexity

2013 ◽  
Vol 41 (4) ◽  
pp. 866-870 ◽  
Author(s):  
Adam E. Hall ◽  
Tamas Dalmay
Keyword(s):  
Gene Regulation ◽  
Small Rnas ◽  
Genome Complexity ◽  
Sequencing Bias ◽  
Non Coding Rnas

The different RNA populations within the cell, or the ‘RNAome’, form a complex and integral layer of gene regulation. In particular, small non-coding RNAs such as microRNAs have been shown to regulate as much as half of all genes expressed in mammals. The recent discovery of novel small RNAs derived from tRNAs, snoRNAs and Y RNAs, as well as the development of techniques that can reduce sequencing bias of these molecules, is slowly helping us to unveil the secrets of the genome.

When junk DNA turns functional: transposon-derived non-coding RNAs in plants

2021 ◽  
Author(s):  
Federico D Ariel ◽  
Pablo A Manavella
Keyword(s):  
Small Rnas ◽  
Genome Instability ◽  
Current Knowledge ◽  
Regulatory Elements ◽  
Rna Molecules ◽  
Genome Complexity ◽  
Protein Partners ◽  
Non Coding Rnas ◽  
Trans Regulation ◽  
Development And Evolution

Abstract Transposable elements (TEs) are major contributors to genome complexity in eukaryotes. TE mobilization may cause genome instability, although it can also drive genome diversity throughout evolution. TE transposition may influence the transcriptional activity of neighboring genes by modulating the epigenomic profile of the region or by altering the relative position of regulatory elements. Notably, TEs have emerged in the last few years as an important source of functional long and small non-coding RNAs. A plethora of small RNAs derived from TEs have been linked to the trans regulation of gene activity at the transcriptional and post-transcriptional levels. Furthermore, TE-derived long non-coding RNAs have been shown to modulate gene expression by interacting with protein partners, sequestering active small RNAs, and forming duplexes with DNA or other RNA molecules. In this review, we summarize our current knowledge of the functional and mechanistic paradigms of TE-derived long and small non-coding RNAs and discuss their role in plant development and evolution.

scholarly journals Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marco Passamonti ◽  
Marco Calderone ◽  
Manuel Delpero ◽  
Federico Plazzi
Keyword(s):  
Gene Regulation ◽  
Nuclear Gene ◽  
Non Coding Rnas ◽  
Nuclear Gene Regulation

scholarly journals Correction: MicroRNAs: small RNAs with a big role in gene regulation

2004 ◽  
Vol 5 (8) ◽  
pp. 631-631 ◽  
Author(s):  
Lin He ◽  
Gregory J Hannon
Keyword(s):  
Gene Regulation ◽  
Small Rnas

scholarly journals Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises

2021 ◽  
Vol 11 ◽  
Author(s):  
Mikel Irastortza-Olaziregi ◽  
Orna Amster-Choder
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Localization ◽  
Molecular Architecture ◽  
Independent Manner ◽  
New Information ◽  
Shed Light

Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming “RNAP.mRNA.ribosome” complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.

The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme

2008 ◽  
Vol 389 (4) ◽  
pp. 323-331 ◽  
Author(s):  
David Umlauf ◽  
Peter Fraser ◽  
Takashi Nagano
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Genome Architecture ◽  
Paradoxical Situation ◽  
Intergenic Regions ◽  
Non Coding Rnas ◽  
Variations On A Theme

Abstract Transcriptome studies have uncovered a plethora of non-coding RNAs (ncRNA) in mammals. Most originate within intergenic regions of the genome and recent evidence indicates that some are involved in many different pathways that ultimately act on genome architecture and gene expression. In this review, we discuss the role of well-characterized long ncRNAs in gene regulation pointing to their similarities, but also their differences. We will attempt to highlight a paradoxical situation in which transcription is needed to repress entire chromosomal domains possibly through the action of ncRNAs that create nuclear environments refractory to transcription.

scholarly journals Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit

2018 ◽  
Vol 114 (11) ◽  
pp. 2530-2539 ◽  
Author(s):  
Niraj Kumar ◽  
Kourosh Zarringhalam ◽  
Rahul V. Kulkarni
Keyword(s):  
Gene Regulation ◽  
Stochastic Modeling ◽  
Strong Interaction ◽  
Small Rnas

scholarly journals Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 459 ◽  
Author(s):  
Priyanka Borah ◽  
Antara Das ◽  
Matthew Milner ◽  
Arif Ali ◽  
Alison Bentley ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Next Generation Sequencing ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Long Non Coding Rna ◽  
Nutrient Homeostasis ◽  
Generation Sequencing

Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.

Circular RNAs as microRNA sponges: evidence and controversies

2021 ◽  
Author(s):  
Morten T. Jarlstad Olesen ◽  
Lasse S. Kristensen
Keyword(s):  
Gene Regulation ◽  
Target Genes ◽  
Research Field ◽  
Circular Rnas ◽  
Transcriptional Level ◽  
Additional Layer ◽  
Complex Process ◽  
Non Coding Rnas ◽  
New Research ◽  
Microrna Sponges

Abstract Gene expression in eukaryotic cells is a complex process encompassing several layers of regulation at the transcriptional and post-transcriptional levels. At the post-transcriptional level, microRNAs (miRs) are key regulatory molecules that function by binding directly to mRNAs. This generally leads to less efficient translation of the target mRNAs. More recently, an additional layer of gene regulation has been discovered, as other molecules, including circular RNAs (circRNAs), may bind to miRs and thereby function as sponges or decoys resulting in increased expression of the corresponding miR target genes. The circRNAs constitute a large class of mainly non-coding RNAs, which have been extensively studied in recent years, in particular in the cancer research field where many circRNAs have been proposed to function as miR sponges. Here, we briefly describe miR-mediated gene regulation and the extra layer of regulation that is imposed by the circRNAs. We describe techniques and methodologies that are commonly used to investigate potential miR sponging properties of circRNAs and discuss major pitfalls and controversies within this relatively new research field.

Dysregulation of miRNA in cancer progression

2021 ◽  
Author(s):  
Rucha P.
Keyword(s):  
Gene Regulation ◽  
Cancer Progression ◽  
Therapeutic Target ◽  
Chromosomal Abnormalities ◽  
Human Cancer ◽  
Epigenetic Modification ◽  
Therapeutic Applications ◽  
Non Coding Rnas ◽  
Transcriptional Gene Regulation

MicroRNAs (miRNAs) are a category of highly conserved tiny non-coding RNAs that play a role in post-transcriptional gene regulation. Numerous studies have shown the role of dysregulated miRNA in a variety of illnesses, including human cancer. MiRNA is dysregulated by a variety of processes, including dysregulation of miRNA synthesis, aberrant miRNA transcription, dysregulated epigenetic modification, and chromosomal abnormalities. MiRNAs that are overexpressed have been shown to influence cancer's hallmarks. Recent research has shown miRNA's potential as a therapeutic target and biomarker. In this review, we discussed the synthesis and regulation of miRNA, as well as its dysregulation in human cancer and other disorders, as well as some of the therapeutic applications of miRNA.

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